Principal Investigator/Program Director (Last, first, middle): Brash, Douglas, E. Project Summary/Abstract Special regions of the genome such as active genes are involved in activating P53 and triggering apoptosis after UV-induced DNA damage. Certain genes sustain DNA damage at higher rates than other genes do after UV or during human aging. Yet our present knowledge of DNA damage and repair processes comes from either whole-cell DNA or from subgene fragments, nucleotide-resolution studies, or protein biochemistry. The present proposal addresses the mesoscopic level of DNA damage and repair lying between these two realms: Do DNA damage and repair rates vary across the genome, in DNA tracts such as telomeres or ribosomal DNA or as revealed by genomic scans of damage and repair across a DNA tiling microarray? Are these variations biologically significant? This proposal uses a newly-developed immunoprecipitation assay, termed IPoD (immunoprecipitation of dimers), which can be used with repeated DNA and which [unreadable] unlike cleavage assays [unreadable] can be applied to microarrays. The Aims include: Measure induction and repair of UVB-induced cyclobutane pyrimidine dimers and (6-4) photoproducts, and oxidant-induced 8-oxo-dG lesions, in telomeres and ribosomal DNA; identify the genes required for telomere repair; extend DNA photoproduct and repair measurements to genomic tiling arrays covering the entire ENCODE (Encyclopedia of DNA Elements) Consortium region; extend to chromosome 22, which contains DNA fragile sites and oncogene breakpoints; and use bioinformatics approaches to correlate the resulting ENCODE 'DNA damage track' and 'DNA repair track' to the ENCODE tracks already studied, which include transcription sites, chromatin-free sites, and replication origins and termini. Together, these studies may reveal both DNA damage and repair variations across the genome and mechanisms underlying them. Project Description Page 6